Starting phenix.real_space_refine
on Tue Feb 11 10:52:42 2025 by dcliebschner
===============================================================================

Processing files:
-------------------------------------------------------------------------------

  Found model, /net/cci-nas-00/data/ceres_data/8eh5_28135/02_2025/8eh5_28135.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8eh5_28135/02_2025/8eh5_28135.map

Processing PHIL parameters:
-------------------------------------------------------------------------------

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.36
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8eh5_28135/02_2025/8eh5_28135.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8eh5_28135/02_2025/8eh5_28135.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8eh5_28135/02_2025/8eh5_28135.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8eh5_28135/02_2025/8eh5_28135.cif"
  }
  resolution = 3.36
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


Starting job
===============================================================================
-------------------------------------------------------------------------------
Citation:
*********
Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams
PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography.
Acta Cryst. D74:531-544.

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.003 sd=   0.064
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 4
    Type Number    sf(0)   Gaussians
     S      24      5.16       5
     C    3481      2.51       5
     N     939      2.21       5
     O    1059      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 34 residue(s): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/chem_data/mon_lib"
  Total number of atoms: 5503
  Number of models: 1
  Model: ""
    Number of chains: 7
    Chain: "G"
      Number of atoms: 187
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 26, 187
          Classifications: {'peptide': 26}
          Link IDs: {'PTRANS': 6, 'TRANS': 19}
    Chain: "H"
      Number of atoms: 940
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 119, 940
          Classifications: {'peptide': 119}
          Link IDs: {'PTRANS': 3, 'TRANS': 115}
    Chain: "L"
      Number of atoms: 832
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 107, 832
          Classifications: {'peptide': 107}
          Link IDs: {'PTRANS': 5, 'TRANS': 101}
    Chain: "M"
      Number of atoms: 940
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 119, 940
          Classifications: {'peptide': 119}
          Link IDs: {'PTRANS': 3, 'TRANS': 115}
    Chain: "N"
      Number of atoms: 832
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 107, 832
          Classifications: {'peptide': 107}
          Link IDs: {'PTRANS': 5, 'TRANS': 101}
    Chain: "O"
      Number of atoms: 940
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 119, 940
          Classifications: {'peptide': 119}
          Link IDs: {'PTRANS': 3, 'TRANS': 115}
    Chain: "P"
      Number of atoms: 832
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 107, 832
          Classifications: {'peptide': 107}
          Link IDs: {'PTRANS': 5, 'TRANS': 101}
  Time building chain proxies: 3.55, per 1000 atoms: 0.65
  Number of scatterers: 5503
  At special positions: 0
  Unit cell: (60.61, 98.23, 109.725, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S      24     16.00
     O    1059      8.00
     N     939      7.00
     C    3481      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=6, symmetry=0
    Simple disulfide: pdb=" SG  CYS H  22 " - pdb=" SG  CYS H  92 " distance=2.02
    Simple disulfide: pdb=" SG  CYS L  23 " - pdb=" SG  CYS L  88 " distance=2.03
    Simple disulfide: pdb=" SG  CYS M  22 " - pdb=" SG  CYS M  92 " distance=2.02
    Simple disulfide: pdb=" SG  CYS N  23 " - pdb=" SG  CYS N  88 " distance=2.03
    Simple disulfide: pdb=" SG  CYS O  22 " - pdb=" SG  CYS O  92 " distance=2.03
    Simple disulfide: pdb=" SG  CYS P  23 " - pdb=" SG  CYS P  88 " distance=2.05

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 1.33
  Conformation dependent library (CDL) restraints added in 714.2 milliseconds
  

  1380 Ramachandran restraints generated.
    690 Oldfield, 0 Emsley, 690 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1276

  Finding SS restraints...
    Secondary structure from input PDB file:
      10 helices and 18 sheets defined
      6.5% alpha, 42.2% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.96
  Creating SS restraints...
    Processing helix  chain 'H' and resid 52 through 55
      removed outlier: 3.964A  pdb=" N   SER H  55 " --> pdb=" O   PHE H  52A" (cutoff:3.500A)
    Processing helix  chain 'H' and resid 61 through 64
    Processing helix  chain 'H' and resid 83 through 87
    Processing helix  chain 'L' and resid 79 through 83
    Processing helix  chain 'M' and resid 53 through 55
      No H-bonds generated for 'chain 'M' and resid 53 through 55'
    Processing helix  chain 'M' and resid 61 through 64
    Processing helix  chain 'M' and resid 83 through 87
    Processing helix  chain 'N' and resid 79 through 83
    Processing helix  chain 'O' and resid 83 through 87
    Processing helix  chain 'P' and resid 79 through 83
    Processing sheet with id=AA1, first strand: chain 'H' and resid 3 through 7
    Processing sheet with id=AA2, first strand: chain 'H' and resid 10 through 11
      removed outlier: 6.103A  pdb=" N   GLY H  10 " --> pdb=" O   THR H 110 " (cutoff:3.500A)
      removed outlier: 6.453A  pdb=" N   MET H  34 " --> pdb=" O   VAL H  50 " (cutoff:3.500A)
      removed outlier: 4.447A  pdb=" N   VAL H  50 " --> pdb=" O   MET H  34 " (cutoff:3.500A)
      removed outlier: 6.577A  pdb=" N   TRP H  36 " --> pdb=" O   VAL H  48 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'H' and resid 96 through 97
      removed outlier: 3.589A  pdb=" N   PHE H  96 " --> pdb=" O   PHE H 100C" (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'L' and resid 5 through 6
    Processing sheet with id=AA5, first strand: chain 'L' and resid 10 through 13
      removed outlier: 5.514A  pdb=" N   LEU L  33 " --> pdb=" O   TYR L  49 " (cutoff:3.500A)
      removed outlier: 5.679A  pdb=" N   TYR L  49 " --> pdb=" O   LEU L  33 " (cutoff:3.500A)
      removed outlier: 6.467A  pdb=" N   TRP L  35 " --> pdb=" O   LEU L  47 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'L' and resid 10 through 13
    Processing sheet with id=AA7, first strand: chain 'M' and resid 3 through 7
    Processing sheet with id=AA8, first strand: chain 'M' and resid 10 through 11
      removed outlier: 6.114A  pdb=" N   GLY M  10 " --> pdb=" O   THR M 110 " (cutoff:3.500A)
      removed outlier: 6.572A  pdb=" N   MET M  34 " --> pdb=" O   VAL M  50 " (cutoff:3.500A)
      removed outlier: 4.484A  pdb=" N   VAL M  50 " --> pdb=" O   MET M  34 " (cutoff:3.500A)
      removed outlier: 6.665A  pdb=" N   TRP M  36 " --> pdb=" O   VAL M  48 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'M' and resid 96 through 97
    Processing sheet with id=AB1, first strand: chain 'N' and resid 4 through 5
    Processing sheet with id=AB2, first strand: chain 'N' and resid 10 through 13
      removed outlier: 5.307A  pdb=" N   LEU N  33 " --> pdb=" O   TYR N  49 " (cutoff:3.500A)
      removed outlier: 5.446A  pdb=" N   TYR N  49 " --> pdb=" O   LEU N  33 " (cutoff:3.500A)
      removed outlier: 6.486A  pdb=" N   TRP N  35 " --> pdb=" O   LEU N  47 " (cutoff:3.500A)
      removed outlier: 3.576A  pdb=" N   LYS N  50 " --> pdb=" O   SER N  53 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'N' and resid 10 through 13
    Processing sheet with id=AB4, first strand: chain 'O' and resid 3 through 7
    Processing sheet with id=AB5, first strand: chain 'O' and resid 10 through 12
      removed outlier: 6.682A  pdb=" N   MET O  34 " --> pdb=" O   VAL O  50 " (cutoff:3.500A)
      removed outlier: 4.484A  pdb=" N   VAL O  50 " --> pdb=" O   MET O  34 " (cutoff:3.500A)
      removed outlier: 6.620A  pdb=" N   TRP O  36 " --> pdb=" O   VAL O  48 " (cutoff:3.500A)
      removed outlier: 4.209A  pdb=" N   TRP O  52 " --> pdb=" O   ASN O  56 " (cutoff:3.500A)
      removed outlier: 5.672A  pdb=" N   ASN O  56 " --> pdb=" O   TRP O  52 " (cutoff:3.500A)
    Processing sheet with id=AB6, first strand: chain 'O' and resid 96 through 98
    Processing sheet with id=AB7, first strand: chain 'P' and resid 4 through 6
    Processing sheet with id=AB8, first strand: chain 'P' and resid 10 through 13
      removed outlier: 4.584A  pdb=" N   LEU P  33 " --> pdb=" O   TYR P  49 " (cutoff:3.500A)
      removed outlier: 5.114A  pdb=" N   TYR P  49 " --> pdb=" O   LEU P  33 " (cutoff:3.500A)
      removed outlier: 6.528A  pdb=" N   TRP P  35 " --> pdb=" O   LEU P  47 " (cutoff:3.500A)
      removed outlier: 6.399A  pdb=" N   SER P  53 " --> pdb=" O   TYR P  49 " (cutoff:3.500A)
    Processing sheet with id=AB9, first strand: chain 'P' and resid 10 through 13

    233 hydrogen bonds defined for protein.
    516 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 1.64

  Time building geometry restraints manager: 1.54 seconds

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.

  Histogram of bond lengths:
        1.18 -     1.31: 950
        1.31 -     1.44: 1715
        1.44 -     1.57: 2910
        1.57 -     1.70: 33
        1.70 -     1.83: 35
  Bond restraints: 5643
  Sorted by residual:
  bond pdb=" CB  HIS O  35 "
       pdb=" CG  HIS O  35 "
    ideal  model  delta    sigma   weight residual
    1.497  1.403  0.094 1.40e-02 5.10e+03 4.52e+01
  bond pdb=" CB  ARG O  38 "
       pdb=" CG  ARG O  38 "
    ideal  model  delta    sigma   weight residual
    1.520  1.353  0.167 3.00e-02 1.11e+03 3.10e+01
  bond pdb=" CB  ARG H  38 "
       pdb=" CG  ARG H  38 "
    ideal  model  delta    sigma   weight residual
    1.520  1.357  0.163 3.00e-02 1.11e+03 2.95e+01
  bond pdb=" CB  PHE O  52A"
       pdb=" CG  PHE O  52A"
    ideal  model  delta    sigma   weight residual
    1.502  1.379  0.123 2.30e-02 1.89e+03 2.86e+01
  bond pdb=" CB  HIS M  93 "
       pdb=" CG  HIS M  93 "
    ideal  model  delta    sigma   weight residual
    1.497  1.423  0.074 1.40e-02 5.10e+03 2.79e+01
  ... (remaining 5638 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.60: 6661
        2.60 -     5.21: 857
        5.21 -     7.81: 128
        7.81 -    10.41: 6
       10.41 -    13.01: 1
  Bond angle restraints: 7653
  Sorted by residual:
  angle pdb=" C   GLY M 100A"
        pdb=" N   PRO M 100B"
        pdb=" CA  PRO M 100B"
      ideal   model   delta    sigma   weight residual
     120.31  127.92   -7.61 9.80e-01 1.04e+00 6.03e+01
  angle pdb=" CA  ASP O  98 "
        pdb=" CB  ASP O  98 "
        pdb=" CG  ASP O  98 "
      ideal   model   delta    sigma   weight residual
     112.60  120.06   -7.46 1.00e+00 1.00e+00 5.57e+01
  angle pdb=" C   TYR H  32 "
        pdb=" CA  TYR H  32 "
        pdb=" CB  TYR H  32 "
      ideal   model   delta    sigma   weight residual
     109.54  122.55  -13.01 1.84e+00 2.95e-01 5.00e+01
  angle pdb=" N   ILE N  29 "
        pdb=" CA  ILE N  29 "
        pdb=" C   ILE N  29 "
      ideal   model   delta    sigma   weight residual
     111.81  106.23    5.58 8.60e-01 1.35e+00 4.22e+01
  angle pdb=" C   GLY O 100A"
        pdb=" N   PRO O 100B"
        pdb=" CA  PRO O 100B"
      ideal   model   delta    sigma   weight residual
     120.14  126.48   -6.34 1.06e+00 8.90e-01 3.58e+01
  ... (remaining 7648 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.98: 3168
       17.98 -    35.96: 85
       35.96 -    53.95: 27
       53.95 -    71.93: 14
       71.93 -    89.91: 4
  Dihedral angle restraints: 3298
    sinusoidal: 1286
      harmonic: 2012
  Sorted by residual:
  dihedral pdb=" CB  CYS N  23 "
           pdb=" SG  CYS N  23 "
           pdb=" SG  CYS N  88 "
           pdb=" CB  CYS N  88 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00  166.66  -73.66     1      1.00e+01 1.00e-02 6.90e+01
  dihedral pdb=" C   TYR H  32 "
           pdb=" N   TYR H  32 "
           pdb=" CA  TYR H  32 "
           pdb=" CB  TYR H  32 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.60 -140.96   18.36     0      2.50e+00 1.60e-01 5.40e+01
  dihedral pdb=" N   TYR H  32 "
           pdb=" C   TYR H  32 "
           pdb=" CA  TYR H  32 "
           pdb=" CB  TYR H  32 "
      ideal   model   delta  harmonic     sigma   weight residual
     122.80  135.69  -12.89     0      2.50e+00 1.60e-01 2.66e+01
  ... (remaining 3295 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.120: 670
       0.120 -    0.239: 130
       0.239 -    0.359: 10
       0.359 -    0.478: 1
       0.478 -    0.598: 1
  Chirality restraints: 812
  Sorted by residual:
  chirality pdb=" CA  TYR H  32 "
            pdb=" N   TYR H  32 "
            pdb=" C   TYR H  32 "
            pdb=" CB  TYR H  32 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    1.91    0.60 2.00e-01 2.50e+01 8.93e+00
  chirality pdb=" CA  ILE H  28 "
            pdb=" N   ILE H  28 "
            pdb=" C   ILE H  28 "
            pdb=" CB  ILE H  28 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.82   -0.38 2.00e-01 2.50e+01 3.65e+00
  chirality pdb=" CA  ARG H  94 "
            pdb=" N   ARG H  94 "
            pdb=" C   ARG H  94 "
            pdb=" CB  ARG H  94 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.87   -0.36 2.00e-01 2.50e+01 3.17e+00
  ... (remaining 809 not shown)

  Planarity restraints: 983
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TRP N  35 "   -0.049 2.00e-02 2.50e+03   2.61e-02 1.71e+01
        pdb=" CG  TRP N  35 "    0.010 2.00e-02 2.50e+03
        pdb=" CD1 TRP N  35 "    0.008 2.00e-02 2.50e+03
        pdb=" CD2 TRP N  35 "    0.029 2.00e-02 2.50e+03
        pdb=" NE1 TRP N  35 "    0.005 2.00e-02 2.50e+03
        pdb=" CE2 TRP N  35 "    0.011 2.00e-02 2.50e+03
        pdb=" CE3 TRP N  35 "    0.039 2.00e-02 2.50e+03
        pdb=" CZ2 TRP N  35 "   -0.019 2.00e-02 2.50e+03
        pdb=" CZ3 TRP N  35 "    0.003 2.00e-02 2.50e+03
        pdb=" CH2 TRP N  35 "   -0.038 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  GLY O 100A"    0.019 2.00e-02 2.50e+03   3.75e-02 1.41e+01
        pdb=" C   GLY O 100A"   -0.065 2.00e-02 2.50e+03
        pdb=" O   GLY O 100A"    0.025 2.00e-02 2.50e+03
        pdb=" N   PRO O 100B"    0.021 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  PRO H 100B"    0.019 2.00e-02 2.50e+03   3.75e-02 1.40e+01
        pdb=" C   PRO H 100B"   -0.065 2.00e-02 2.50e+03
        pdb=" O   PRO H 100B"    0.024 2.00e-02 2.50e+03
        pdb=" N   PHE H 100C"    0.022 2.00e-02 2.50e+03
  ... (remaining 980 not shown)

  Histogram of nonbonded interaction distances:
        2.24 -     2.77: 1134
        2.77 -     3.30: 4662
        3.30 -     3.83: 9543
        3.83 -     4.37: 11595
        4.37 -     4.90: 19224
  Nonbonded interactions: 46158
  Sorted by model distance:
  nonbonded pdb=" OH  TYR H 102 "
            pdb=" OG  SER P  67 "
     model   vdw
     2.236 3.040
  nonbonded pdb=" N   ASP H 101 "
            pdb=" OD1 ASP H 101 "
     model   vdw
     2.412 3.120
  nonbonded pdb=" OD2 ASP O  72 "
            pdb=" NZ  LYS O  75 "
     model   vdw
     2.424 3.120
  nonbonded pdb=" OD2 ASP H  72 "
            pdb=" NZ  LYS H  75 "
     model   vdw
     2.429 3.120
  nonbonded pdb=" O   TYR H  32 "
            pdb=" NH1 ARG H  94 "
     model   vdw
     2.432 3.120
  ... (remaining 46153 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
Found NCS groups:
ncs_group {
  reference = chain 'H'
  selection = chain 'M'
  selection = chain 'O'
}
ncs_group {
  reference = chain 'L'
  selection = chain 'N'
  selection = chain 'P'
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             0.390
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.020
  Extract box with map and model:          0.190
  Check model and map are aligned:         0.040
  Set scattering table:                    0.050
  Process input model:                     16.860
  Find NCS groups from input model:        0.180
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:2.740
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   20.490
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7462
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.023   0.167   5643  Z= 1.446
  Angle     :  1.807  13.013   7653  Z= 1.206
  Chirality :  0.094   0.598    812
  Planarity :  0.008   0.043    983
  Dihedral  : 10.683  89.909   2004
  Min Nonbonded Distance : 2.236

Molprobity Statistics.
  All-atom Clashscore : 2.69
  Ramachandran Plot:
    Outliers :  0.58 %
    Allowed  :  3.91 %
    Favored  : 95.51 %
  Rotamer:
    Outliers :  0.50 %
    Allowed  :  0.84 %
    Favored  : 98.66 %
  Cbeta Deviations :  0.16 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.43 (0.32), residues: 690
  helix:  None (None), residues: 0
  sheet: -0.35 (0.29), residues: 282
  loop :  0.98 (0.33), residues: 408

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.049   0.009   TRP N  35 
 HIS   0.011   0.003   HIS H  93 
 PHE   0.033   0.006   PHE N  98 
 TYR   0.043   0.006   TYR N  49 
 ARG   0.007   0.001   ARG O  38 

*********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  1380 Ramachandran restraints generated.
    690 Oldfield, 0 Emsley, 690 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1380 Ramachandran restraints generated.
    690 Oldfield, 0 Emsley, 690 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  190 residues out of total 598 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 187
  time to evaluate  : 0.548 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: H   93 HIS cc_start: 0.6970 (OUTLIER) cc_final: 0.6346 (t70)
REVERT: H   95 ASN cc_start: 0.7541 (OUTLIER) cc_final: 0.6998 (t0)
REVERT: L    4 MET cc_start: 0.8205 (mmm) cc_final: 0.7943 (mmm)
REVERT: M   68 THR cc_start: 0.7417 (m) cc_final: 0.7096 (p)
REVERT: M   77 THR cc_start: 0.6485 (m) cc_final: 0.6100 (m)
REVERT: N   24 ARG cc_start: 0.8107 (mtt-85) cc_final: 0.7473 (ttt90)
REVERT: O   46 GLU cc_start: 0.7849 (tt0) cc_final: 0.7438 (mt-10)
REVERT: P   72 THR cc_start: 0.8330 (m) cc_final: 0.8003 (p)
  outliers start: 3
  outliers final: 0
  residues processed: 189
  average time/residue: 0.2165
  time to fit residues: 50.2978
Evaluate side-chains
  128 residues out of total 598 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 126
  time to evaluate  : 0.624 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain H residue   93 HIS
Chi-restraints excluded: chain H residue   95 ASN
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 65
   random chunks:
   chunk 54 optimal weight:    0.9990
   chunk 49 optimal weight:    3.9990
   chunk 27 optimal weight:    0.9980
   chunk 16 optimal weight:    0.6980
   chunk 33 optimal weight:    0.7980
   chunk 26 optimal weight:    0.9990
   chunk 50 optimal weight:    2.9990
   chunk 19 optimal weight:    9.9990
   chunk 30 optimal weight:    5.9990
   chunk 37 optimal weight:    0.9990
   chunk 59 optimal weight:    0.6980
   overall best weight:    0.8382

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Flipped N/Q/H residues before XYZ refinement:
** H  93 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
M   1 GLN
M  76 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4126 r_free = 0.4126 target = 0.165778 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3811 r_free = 0.3811 target = 0.137406 restraints weight = 7425.767|
|-----------------------------------------------------------------------------|
r_work (start): 0.3853 rms_B_bonded: 2.56
r_work: 0.3737 rms_B_bonded: 3.10 restraints_weight: 0.5000
r_work (final): 0.3737
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7221
moved from start:          0.3414

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.068   5643  Z= 0.217
  Angle     :  0.687   8.950   7653  Z= 0.371
  Chirality :  0.048   0.205    812
  Planarity :  0.005   0.026    983
  Dihedral  :  5.655  45.457    776
  Min Nonbonded Distance : 2.459

Molprobity Statistics.
  All-atom Clashscore : 10.76
  Ramachandran Plot:
    Outliers :  0.14 %
    Allowed  :  3.33 %
    Favored  : 96.52 %
  Rotamer:
    Outliers :  1.84 %
    Allowed  :  9.20 %
    Favored  : 88.96 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.32 (0.34), residues: 690
  helix:  None (None), residues: 0
  sheet:  0.09 (0.29), residues: 291
  loop :  0.47 (0.35), residues: 399

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.023   0.001   TRP M  52 
 HIS   0.007   0.002   HIS H  93 
 PHE   0.020   0.002   PHE O 100C
 TYR   0.026   0.002   TYR M  32 
 ARG   0.006   0.001   ARG M  19 

*********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  1380 Ramachandran restraints generated.
    690 Oldfield, 0 Emsley, 690 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1380 Ramachandran restraints generated.
    690 Oldfield, 0 Emsley, 690 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  150 residues out of total 598 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 139
  time to evaluate  : 0.581 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: H   43 LYS cc_start: 0.7922 (mttp) cc_final: 0.7631 (mtmm)
REVERT: H   83 ARG cc_start: 0.7606 (tpt170) cc_final: 0.7046 (mmt-90)
REVERT: H   93 HIS cc_start: 0.7025 (OUTLIER) cc_final: 0.6300 (t70)
REVERT: H  101 ASP cc_start: 0.7736 (p0) cc_final: 0.7307 (p0)
REVERT: L   61 ARG cc_start: 0.8120 (mtm-85) cc_final: 0.7873 (mtm180)
REVERT: M   34 MET cc_start: 0.7909 (tpp) cc_final: 0.7694 (mtt)
REVERT: N   24 ARG cc_start: 0.7341 (mtt-85) cc_final: 0.6377 (ttt90)
REVERT: O  102 TYR cc_start: 0.6881 (m-80) cc_final: 0.6665 (m-10)
REVERT: P    3 GLN cc_start: 0.7371 (mp10) cc_final: 0.7041 (mp10)
REVERT: P    4 MET cc_start: 0.8307 (OUTLIER) cc_final: 0.7830 (mtp)
REVERT: P   24 ARG cc_start: 0.7873 (mtt-85) cc_final: 0.7007 (tpt170)
REVERT: P   72 THR cc_start: 0.8112 (m) cc_final: 0.7585 (p)
  outliers start: 11
  outliers final: 5
  residues processed: 145
  average time/residue: 0.2137
  time to fit residues: 38.4828
Evaluate side-chains
  127 residues out of total 598 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 120
  time to evaluate  : 0.671 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain H residue   93 HIS
Chi-restraints excluded: chain L residue    5 THR
Chi-restraints excluded: chain L residue   63 SER
Chi-restraints excluded: chain L residue   74 THR
Chi-restraints excluded: chain N residue   74 THR
Chi-restraints excluded: chain O residue   31 THR
Chi-restraints excluded: chain P residue    4 MET
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 65
   random chunks:
   chunk 33 optimal weight:    0.9980
   chunk 49 optimal weight:    5.9990
   chunk 25 optimal weight:    7.9990
   chunk 64 optimal weight:    5.9990
   chunk 22 optimal weight:    4.9990
   chunk 19 optimal weight:    0.4980
   chunk 44 optimal weight:    7.9990
   chunk 45 optimal weight:    0.0170
   chunk 24 optimal weight:    8.9990
   chunk 26 optimal weight:    5.9990
   chunk 13 optimal weight:    2.9990
   overall best weight:    1.9022

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Flipped N/Q/H residues before XYZ refinement:
G 109 ASN
** H  93 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
L  70 HIS
** O  76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4086 r_free = 0.4086 target = 0.161832 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3760 r_free = 0.3760 target = 0.133973 restraints weight = 7447.322|
|-----------------------------------------------------------------------------|
r_work (start): 0.3765 rms_B_bonded: 2.47
r_work: 0.3650 rms_B_bonded: 3.01 restraints_weight: 0.5000
r_work: 0.3495 rms_B_bonded: 4.99 restraints_weight: 0.2500
r_work (final): 0.3495
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7529
moved from start:          0.4109

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.081   5643  Z= 0.293
  Angle     :  0.680   8.192   7653  Z= 0.369
  Chirality :  0.048   0.173    812
  Planarity :  0.005   0.029    983
  Dihedral  :  5.536  48.206    774
  Min Nonbonded Distance : 2.425

Molprobity Statistics.
  All-atom Clashscore : 10.95
  Ramachandran Plot:
    Outliers :  0.14 %
    Allowed  :  5.51 %
    Favored  : 94.35 %
  Rotamer:
    Outliers :  3.85 %
    Allowed  : 11.54 %
    Favored  : 84.62 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.02 (0.33), residues: 690
  helix:  None (None), residues: 0
  sheet:  0.08 (0.30), residues: 291
  loop :  0.03 (0.35), residues: 399

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.026   0.002   TRP O  52 
 HIS   0.008   0.002   HIS H  93 
 PHE   0.020   0.002   PHE O  52A
 TYR   0.026   0.002   TYR N  49 
 ARG   0.004   0.001   ARG M  94 

*********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  1380 Ramachandran restraints generated.
    690 Oldfield, 0 Emsley, 690 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1380 Ramachandran restraints generated.
    690 Oldfield, 0 Emsley, 690 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  143 residues out of total 598 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 120
  time to evaluate  : 0.628 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: H   18 LEU cc_start: 0.7941 (OUTLIER) cc_final: 0.7356 (tt)
REVERT: H   43 LYS cc_start: 0.7895 (mttp) cc_final: 0.7640 (mtmm)
REVERT: H   83 ARG cc_start: 0.8134 (tpt170) cc_final: 0.7334 (mmt180)
REVERT: H   93 HIS cc_start: 0.7177 (OUTLIER) cc_final: 0.6454 (t70)
REVERT: H  101 ASP cc_start: 0.7873 (p0) cc_final: 0.7488 (p0)
REVERT: L   82 ASP cc_start: 0.8321 (OUTLIER) cc_final: 0.7578 (m-30)
REVERT: M   85 GLU cc_start: 0.7974 (tm-30) cc_final: 0.7572 (tm-30)
REVERT: N   24 ARG cc_start: 0.7477 (mtt-85) cc_final: 0.6436 (ttt90)
REVERT: N   49 TYR cc_start: 0.6696 (OUTLIER) cc_final: 0.5455 (t80)
REVERT: N   89 GLN cc_start: 0.7199 (OUTLIER) cc_final: 0.6662 (tp40)
REVERT: P    4 MET cc_start: 0.8494 (OUTLIER) cc_final: 0.8050 (mtp)
REVERT: P   18 ARG cc_start: 0.8765 (ttp80) cc_final: 0.8510 (mtp-110)
REVERT: P   72 THR cc_start: 0.8324 (m) cc_final: 0.7789 (p)
  outliers start: 23
  outliers final: 11
  residues processed: 131
  average time/residue: 0.2251
  time to fit residues: 36.2138
Evaluate side-chains
  127 residues out of total 598 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 110
  time to evaluate  : 0.649 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain G residue  109 ASN
Chi-restraints excluded: chain H residue   18 LEU
Chi-restraints excluded: chain H residue   31 THR
Chi-restraints excluded: chain H residue   63 VAL
Chi-restraints excluded: chain H residue   93 HIS
Chi-restraints excluded: chain L residue   26 SER
Chi-restraints excluded: chain L residue   49 TYR
Chi-restraints excluded: chain L residue   74 THR
Chi-restraints excluded: chain L residue   82 ASP
Chi-restraints excluded: chain M residue   69 ILE
Chi-restraints excluded: chain N residue   49 TYR
Chi-restraints excluded: chain N residue   74 THR
Chi-restraints excluded: chain N residue   89 GLN
Chi-restraints excluded: chain O residue   31 THR
Chi-restraints excluded: chain O residue   66 ARG
Chi-restraints excluded: chain O residue   82 MET
Chi-restraints excluded: chain P residue    4 MET
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 65
   random chunks:
   chunk 33 optimal weight:    3.9990
   chunk 27 optimal weight:    5.9990
   chunk 48 optimal weight:    3.9990
   chunk 46 optimal weight:    0.0670
   chunk 9 optimal weight:    0.7980
   chunk 19 optimal weight:    3.9990
   chunk 47 optimal weight:    2.9990
   chunk 40 optimal weight:   20.0000
   chunk 18 optimal weight:    0.9990
   chunk 28 optimal weight:   10.0000
   chunk 62 optimal weight:    5.9990
   overall best weight:    1.7724

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Flipped N/Q/H residues before XYZ refinement:
G 109 ASN
G 129 ASN
** H  93 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
M   1 GLN
O  76 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4076 r_free = 0.4076 target = 0.160940 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3747 r_free = 0.3747 target = 0.132691 restraints weight = 7606.598|
|-----------------------------------------------------------------------------|
r_work (start): 0.3752 rms_B_bonded: 2.55
r_work: 0.3640 rms_B_bonded: 3.05 restraints_weight: 0.5000
r_work (final): 0.3640
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7399
moved from start:          0.4525

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.071   5643  Z= 0.268
  Angle     :  0.644   7.705   7653  Z= 0.347
  Chirality :  0.047   0.167    812
  Planarity :  0.005   0.048    983
  Dihedral  :  5.547  51.287    774
  Min Nonbonded Distance : 2.406

Molprobity Statistics.
  All-atom Clashscore : 11.69
  Ramachandran Plot:
    Outliers :  0.14 %
    Allowed  :  5.80 %
    Favored  : 94.06 %
  Rotamer:
    Outliers :  4.35 %
    Allowed  : 11.54 %
    Favored  : 84.11 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.20 (0.34), residues: 690
  helix:  None (None), residues: 0
  sheet:  0.06 (0.30), residues: 291
  loop : -0.19 (0.35), residues: 399

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP O  52 
 HIS   0.008   0.002   HIS H  93 
 PHE   0.020   0.002   PHE O  52A
 TYR   0.022   0.002   TYR N  49 
 ARG   0.006   0.000   ARG N  31 

*********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  1380 Ramachandran restraints generated.
    690 Oldfield, 0 Emsley, 690 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1380 Ramachandran restraints generated.
    690 Oldfield, 0 Emsley, 690 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  141 residues out of total 598 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 115
  time to evaluate  : 0.761 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: H   43 LYS cc_start: 0.7987 (mttp) cc_final: 0.7694 (mtmm)
REVERT: H   83 ARG cc_start: 0.8004 (tpt170) cc_final: 0.7448 (mmt180)
REVERT: H   93 HIS cc_start: 0.7196 (OUTLIER) cc_final: 0.6160 (t70)
REVERT: H  101 ASP cc_start: 0.7714 (p0) cc_final: 0.7066 (p0)
REVERT: M   85 GLU cc_start: 0.7891 (tm-30) cc_final: 0.7353 (tm-30)
REVERT: N    4 MET cc_start: 0.6453 (mmm) cc_final: 0.5547 (mmm)
REVERT: N   89 GLN cc_start: 0.7256 (OUTLIER) cc_final: 0.6746 (tp40)
REVERT: N  102 THR cc_start: 0.7644 (OUTLIER) cc_final: 0.7383 (p)
REVERT: O    7 SER cc_start: 0.7927 (t) cc_final: 0.7725 (p)
REVERT: O   85 GLU cc_start: 0.6739 (OUTLIER) cc_final: 0.6282 (pm20)
REVERT: P    3 GLN cc_start: 0.7230 (mp10) cc_final: 0.6616 (mp10)
REVERT: P    4 MET cc_start: 0.8258 (OUTLIER) cc_final: 0.7787 (mtp)
REVERT: P   18 ARG cc_start: 0.8788 (ttp80) cc_final: 0.8580 (mtp-110)
REVERT: P   72 THR cc_start: 0.8182 (m) cc_final: 0.7661 (p)
  outliers start: 26
  outliers final: 16
  residues processed: 126
  average time/residue: 0.2479
  time to fit residues: 37.6828
Evaluate side-chains
  129 residues out of total 598 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 108
  time to evaluate  : 0.585 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain H residue   31 THR
Chi-restraints excluded: chain H residue   63 VAL
Chi-restraints excluded: chain H residue   82 MET
Chi-restraints excluded: chain H residue   93 HIS
Chi-restraints excluded: chain L residue    5 THR
Chi-restraints excluded: chain L residue   26 SER
Chi-restraints excluded: chain L residue   49 TYR
Chi-restraints excluded: chain L residue   58 VAL
Chi-restraints excluded: chain L residue   74 THR
Chi-restraints excluded: chain L residue   82 ASP
Chi-restraints excluded: chain M residue   69 ILE
Chi-restraints excluded: chain N residue    2 ILE
Chi-restraints excluded: chain N residue   74 THR
Chi-restraints excluded: chain N residue   89 GLN
Chi-restraints excluded: chain N residue  102 THR
Chi-restraints excluded: chain O residue   12 VAL
Chi-restraints excluded: chain O residue   31 THR
Chi-restraints excluded: chain O residue   48 VAL
Chi-restraints excluded: chain O residue   85 GLU
Chi-restraints excluded: chain P residue    4 MET
Chi-restraints excluded: chain P residue    7 SER
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 65
   random chunks:
   chunk 0 optimal weight:   10.0000
   chunk 60 optimal weight:    3.9990
   chunk 57 optimal weight:    2.9990
   chunk 16 optimal weight:    3.9990
   chunk 38 optimal weight:    6.9990
   chunk 59 optimal weight:    0.7980
   chunk 23 optimal weight:    6.9990
   chunk 37 optimal weight:    0.9990
   chunk 33 optimal weight:    0.8980
   chunk 40 optimal weight:   10.0000
   chunk 7 optimal weight:    0.7980
   overall best weight:    1.2984

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Flipped N/Q/H residues before XYZ refinement:
G 109 ASN
G 113 ASN
** H  93 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4097 r_free = 0.4097 target = 0.162953 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 54)----------------|
| r_work = 0.3771 r_free = 0.3771 target = 0.134758 restraints weight = 7503.837|
|-----------------------------------------------------------------------------|
r_work (start): 0.3773 rms_B_bonded: 2.54
r_work: 0.3661 rms_B_bonded: 3.03 restraints_weight: 0.5000
r_work (final): 0.3661
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7378
moved from start:          0.4797

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.059   5643  Z= 0.219
  Angle     :  0.611   7.691   7653  Z= 0.326
  Chirality :  0.046   0.150    812
  Planarity :  0.004   0.036    983
  Dihedral  :  5.451  54.898    774
  Min Nonbonded Distance : 2.304

Molprobity Statistics.
  All-atom Clashscore : 11.13
  Ramachandran Plot:
    Outliers :  0.14 %
    Allowed  :  5.36 %
    Favored  : 94.49 %
  Rotamer:
    Outliers :  4.18 %
    Allowed  : 12.88 %
    Favored  : 82.94 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.21 (0.34), residues: 690
  helix:  None (None), residues: 0
  sheet:  0.25 (0.29), residues: 324
  loop : -0.43 (0.37), residues: 366

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP O  52 
 HIS   0.008   0.002   HIS H  93 
 PHE   0.015   0.002   PHE O  52A
 TYR   0.016   0.002   TYR P  49 
 ARG   0.006   0.000   ARG N  31 

*********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  1380 Ramachandran restraints generated.
    690 Oldfield, 0 Emsley, 690 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1380 Ramachandran restraints generated.
    690 Oldfield, 0 Emsley, 690 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  135 residues out of total 598 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 110
  time to evaluate  : 0.581 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: H   43 LYS cc_start: 0.8098 (mttp) cc_final: 0.7822 (mtmm)
REVERT: H   83 ARG cc_start: 0.8057 (tpt170) cc_final: 0.7527 (mmt180)
REVERT: L    4 MET cc_start: 0.8433 (mmm) cc_final: 0.8008 (mmm)
REVERT: M   77 THR cc_start: 0.6994 (p) cc_final: 0.6694 (p)
REVERT: M   85 GLU cc_start: 0.7906 (tm-30) cc_final: 0.7311 (tm-30)
REVERT: N   89 GLN cc_start: 0.7241 (OUTLIER) cc_final: 0.6538 (tp40)
REVERT: N  102 THR cc_start: 0.7581 (OUTLIER) cc_final: 0.7360 (p)
REVERT: O   83 ARG cc_start: 0.8199 (mmm160) cc_final: 0.7629 (mmm160)
REVERT: O   85 GLU cc_start: 0.6652 (OUTLIER) cc_final: 0.6153 (pm20)
REVERT: P    3 GLN cc_start: 0.7023 (mp10) cc_final: 0.6432 (mp10)
REVERT: P    4 MET cc_start: 0.8305 (OUTLIER) cc_final: 0.7773 (mtp)
REVERT: P   72 THR cc_start: 0.8092 (m) cc_final: 0.7586 (p)
  outliers start: 25
  outliers final: 18
  residues processed: 125
  average time/residue: 0.2228
  time to fit residues: 34.3678
Evaluate side-chains
  124 residues out of total 598 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 102
  time to evaluate  : 0.487 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain G residue  109 ASN
Chi-restraints excluded: chain G residue  113 ASN
Chi-restraints excluded: chain H residue   31 THR
Chi-restraints excluded: chain H residue   63 VAL
Chi-restraints excluded: chain H residue   82 MET
Chi-restraints excluded: chain H residue   93 HIS
Chi-restraints excluded: chain L residue    5 THR
Chi-restraints excluded: chain L residue   26 SER
Chi-restraints excluded: chain L residue   58 VAL
Chi-restraints excluded: chain L residue   74 THR
Chi-restraints excluded: chain M residue   69 ILE
Chi-restraints excluded: chain N residue   74 THR
Chi-restraints excluded: chain N residue   89 GLN
Chi-restraints excluded: chain N residue  102 THR
Chi-restraints excluded: chain O residue   12 VAL
Chi-restraints excluded: chain O residue   31 THR
Chi-restraints excluded: chain O residue   48 VAL
Chi-restraints excluded: chain O residue   78 VAL
Chi-restraints excluded: chain O residue   85 GLU
Chi-restraints excluded: chain P residue    4 MET
Chi-restraints excluded: chain P residue    7 SER
Chi-restraints excluded: chain P residue   19 VAL
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 65
   random chunks:
   chunk 35 optimal weight:   20.0000
   chunk 32 optimal weight:    3.9990
   chunk 24 optimal weight:    1.9990
   chunk 47 optimal weight:    0.9980
   chunk 63 optimal weight:    3.9990
   chunk 38 optimal weight:    0.8980
   chunk 52 optimal weight:    6.9990
   chunk 31 optimal weight:    1.9990
   chunk 1 optimal weight:    0.7980
   chunk 30 optimal weight:    5.9990
   chunk 40 optimal weight:    7.9990
   overall best weight:    1.3384

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Flipped N/Q/H residues before XYZ refinement:
G 109 ASN
** H  93 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
M 105 GLN
** O  76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4093 r_free = 0.4093 target = 0.162465 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3770 r_free = 0.3770 target = 0.134294 restraints weight = 7469.495|
|-----------------------------------------------------------------------------|
r_work (start): 0.3774 rms_B_bonded: 2.52
r_work: 0.3663 rms_B_bonded: 3.02 restraints_weight: 0.5000
r_work (final): 0.3663
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7384
moved from start:          0.4994

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.059   5643  Z= 0.220
  Angle     :  0.606   7.603   7653  Z= 0.324
  Chirality :  0.046   0.137    812
  Planarity :  0.005   0.036    983
  Dihedral  :  5.556  59.696    774
  Min Nonbonded Distance : 2.429

Molprobity Statistics.
  All-atom Clashscore : 11.59
  Ramachandran Plot:
    Outliers :  0.14 %
    Allowed  :  6.38 %
    Favored  : 93.48 %
  Rotamer:
    Outliers :  4.68 %
    Allowed  : 12.04 %
    Favored  : 83.28 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.19 (0.34), residues: 690
  helix:  None (None), residues: 0
  sheet:  0.36 (0.29), residues: 324
  loop : -0.52 (0.37), residues: 366

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.001   TRP O  36 
 HIS   0.008   0.002   HIS H  93 
 PHE   0.017   0.002   PHE M 100C
 TYR   0.021   0.002   TYR M  32 
 ARG   0.004   0.000   ARG L  61 

*********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  1380 Ramachandran restraints generated.
    690 Oldfield, 0 Emsley, 690 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1380 Ramachandran restraints generated.
    690 Oldfield, 0 Emsley, 690 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  132 residues out of total 598 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 104
  time to evaluate  : 0.589 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: H   18 LEU cc_start: 0.8047 (OUTLIER) cc_final: 0.7403 (tt)
REVERT: H   43 LYS cc_start: 0.8081 (mttp) cc_final: 0.7834 (mtmm)
REVERT: L    4 MET cc_start: 0.8503 (mmm) cc_final: 0.7972 (mmm)
REVERT: L   31 ARG cc_start: 0.8406 (ttm-80) cc_final: 0.8101 (ttm110)
REVERT: M   85 GLU cc_start: 0.7905 (tm-30) cc_final: 0.7284 (tm-30)
REVERT: N   89 GLN cc_start: 0.7419 (OUTLIER) cc_final: 0.6812 (tp40)
REVERT: N  102 THR cc_start: 0.7654 (OUTLIER) cc_final: 0.7381 (p)
REVERT: O   83 ARG cc_start: 0.8278 (mmm160) cc_final: 0.7658 (mmm160)
REVERT: O   85 GLU cc_start: 0.6675 (OUTLIER) cc_final: 0.6169 (pm20)
REVERT: P    3 GLN cc_start: 0.6974 (mp10) cc_final: 0.6415 (mp10)
REVERT: P    4 MET cc_start: 0.8309 (OUTLIER) cc_final: 0.7505 (mtm)
REVERT: P   72 THR cc_start: 0.8096 (m) cc_final: 0.7593 (p)
  outliers start: 28
  outliers final: 19
  residues processed: 120
  average time/residue: 0.2236
  time to fit residues: 33.3946
Evaluate side-chains
  124 residues out of total 598 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 100
  time to evaluate  : 0.637 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain G residue  109 ASN
Chi-restraints excluded: chain H residue   18 LEU
Chi-restraints excluded: chain H residue   31 THR
Chi-restraints excluded: chain H residue   63 VAL
Chi-restraints excluded: chain H residue   82 MET
Chi-restraints excluded: chain H residue   93 HIS
Chi-restraints excluded: chain L residue    5 THR
Chi-restraints excluded: chain L residue   26 SER
Chi-restraints excluded: chain L residue   58 VAL
Chi-restraints excluded: chain L residue   74 THR
Chi-restraints excluded: chain M residue   69 ILE
Chi-restraints excluded: chain N residue   74 THR
Chi-restraints excluded: chain N residue   89 GLN
Chi-restraints excluded: chain N residue  102 THR
Chi-restraints excluded: chain O residue   12 VAL
Chi-restraints excluded: chain O residue   31 THR
Chi-restraints excluded: chain O residue   48 VAL
Chi-restraints excluded: chain O residue   78 VAL
Chi-restraints excluded: chain O residue   85 GLU
Chi-restraints excluded: chain P residue    4 MET
Chi-restraints excluded: chain P residue    7 SER
Chi-restraints excluded: chain P residue   19 VAL
Chi-restraints excluded: chain P residue   69 THR
Chi-restraints excluded: chain P residue   90 GLU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 65
   random chunks:
   chunk 11 optimal weight:    3.9990
   chunk 13 optimal weight:    2.9990
   chunk 56 optimal weight:    2.9990
   chunk 2 optimal weight:    0.8980
   chunk 43 optimal weight:    4.9990
   chunk 10 optimal weight:    1.9990
   chunk 27 optimal weight:    0.8980
   chunk 23 optimal weight:    5.9990
   chunk 26 optimal weight:    4.9990
   chunk 3 optimal weight:    3.9990
   chunk 21 optimal weight:    0.9990
   overall best weight:    1.5586

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Flipped N/Q/H residues before XYZ refinement:
G 109 ASN
** H  93 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
M 105 GLN
** O  76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4077 r_free = 0.4077 target = 0.161054 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3775 r_free = 0.3775 target = 0.134724 restraints weight = 7444.718|
|-----------------------------------------------------------------------------|
r_work (start): 0.3780 rms_B_bonded: 2.24
r_work: 0.3672 rms_B_bonded: 2.73 restraints_weight: 0.5000
r_work: 0.3524 rms_B_bonded: 4.55 restraints_weight: 0.2500
r_work (final): 0.3524
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7530
moved from start:          0.5136

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.065   5643  Z= 0.239
  Angle     :  0.603   8.086   7653  Z= 0.322
  Chirality :  0.046   0.143    812
  Planarity :  0.005   0.041    983
  Dihedral  :  5.486  55.543    774
  Min Nonbonded Distance : 2.449

Molprobity Statistics.
  All-atom Clashscore : 11.78
  Ramachandran Plot:
    Outliers :  0.14 %
    Allowed  :  6.67 %
    Favored  : 93.19 %
  Rotamer:
    Outliers :  5.18 %
    Allowed  : 12.21 %
    Favored  : 82.61 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.22 (0.34), residues: 690
  helix:  None (None), residues: 0
  sheet:  0.39 (0.29), residues: 324
  loop : -0.61 (0.37), residues: 366

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.020   0.001   TRP O  36 
 HIS   0.008   0.002   HIS H  93 
 PHE   0.014   0.002   PHE M 100C
 TYR   0.018   0.002   TYR N  49 
 ARG   0.004   0.000   ARG P  96 

*********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  1380 Ramachandran restraints generated.
    690 Oldfield, 0 Emsley, 690 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1380 Ramachandran restraints generated.
    690 Oldfield, 0 Emsley, 690 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  140 residues out of total 598 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 109
  time to evaluate  : 0.649 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: H   18 LEU cc_start: 0.8042 (OUTLIER) cc_final: 0.7395 (tt)
REVERT: H   43 LYS cc_start: 0.8076 (mttp) cc_final: 0.7822 (mtmm)
REVERT: M   77 THR cc_start: 0.7071 (p) cc_final: 0.6870 (p)
REVERT: M   85 GLU cc_start: 0.7797 (tm-30) cc_final: 0.7089 (tm-30)
REVERT: N    4 MET cc_start: 0.6899 (mmm) cc_final: 0.6381 (mmm)
REVERT: N   89 GLN cc_start: 0.7538 (OUTLIER) cc_final: 0.6844 (tp40)
REVERT: N  102 THR cc_start: 0.7592 (OUTLIER) cc_final: 0.7334 (p)
REVERT: O   83 ARG cc_start: 0.8410 (mmm160) cc_final: 0.7728 (mmm160)
REVERT: O   85 GLU cc_start: 0.6744 (OUTLIER) cc_final: 0.6243 (pm20)
REVERT: P    3 GLN cc_start: 0.7167 (mp10) cc_final: 0.6581 (mp10)
REVERT: P    4 MET cc_start: 0.8468 (OUTLIER) cc_final: 0.7684 (mtm)
REVERT: P   72 THR cc_start: 0.8302 (m) cc_final: 0.7796 (p)
  outliers start: 31
  outliers final: 20
  residues processed: 128
  average time/residue: 0.2092
  time to fit residues: 33.6097
Evaluate side-chains
  128 residues out of total 598 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 103
  time to evaluate  : 0.622 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain G residue  109 ASN
Chi-restraints excluded: chain H residue   18 LEU
Chi-restraints excluded: chain H residue   31 THR
Chi-restraints excluded: chain H residue   63 VAL
Chi-restraints excluded: chain H residue   93 HIS
Chi-restraints excluded: chain L residue    5 THR
Chi-restraints excluded: chain L residue   26 SER
Chi-restraints excluded: chain L residue   49 TYR
Chi-restraints excluded: chain L residue   58 VAL
Chi-restraints excluded: chain L residue   74 THR
Chi-restraints excluded: chain M residue   69 ILE
Chi-restraints excluded: chain N residue   74 THR
Chi-restraints excluded: chain N residue   89 GLN
Chi-restraints excluded: chain N residue  102 THR
Chi-restraints excluded: chain O residue    7 SER
Chi-restraints excluded: chain O residue   12 VAL
Chi-restraints excluded: chain O residue   31 THR
Chi-restraints excluded: chain O residue   48 VAL
Chi-restraints excluded: chain O residue   78 VAL
Chi-restraints excluded: chain O residue   85 GLU
Chi-restraints excluded: chain P residue    4 MET
Chi-restraints excluded: chain P residue    7 SER
Chi-restraints excluded: chain P residue   19 VAL
Chi-restraints excluded: chain P residue   69 THR
Chi-restraints excluded: chain P residue   90 GLU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 65
   random chunks:
   chunk 50 optimal weight:    5.9990
   chunk 35 optimal weight:    4.9990
   chunk 14 optimal weight:    0.4980
   chunk 37 optimal weight:    0.5980
   chunk 13 optimal weight:    0.4980
   chunk 32 optimal weight:    0.9980
   chunk 1 optimal weight:    7.9990
   chunk 40 optimal weight:    0.4980
   chunk 48 optimal weight:    0.6980
   chunk 7 optimal weight:    0.0970
   chunk 51 optimal weight:    8.9990
   overall best weight:    0.4378

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Flipped N/Q/H residues before XYZ refinement:
G 109 ASN
H  93 HIS
L   6 GLN
M  95 ASN
M 105 GLN
** O  76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4142 r_free = 0.4142 target = 0.166850 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3838 r_free = 0.3838 target = 0.139611 restraints weight = 7402.931|
|-----------------------------------------------------------------------------|
r_work (start): 0.3838 rms_B_bonded: 2.49
r_work: 0.3728 rms_B_bonded: 2.99 restraints_weight: 0.5000
r_work: 0.3576 rms_B_bonded: 4.98 restraints_weight: 0.2500
r_work (final): 0.3576
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7439
moved from start:          0.5409

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.032   5643  Z= 0.146
  Angle     :  0.573   9.437   7653  Z= 0.304
  Chirality :  0.045   0.137    812
  Planarity :  0.004   0.043    983
  Dihedral  :  4.797  40.831    774
  Min Nonbonded Distance : 2.494

Molprobity Statistics.
  All-atom Clashscore : 10.85
  Ramachandran Plot:
    Outliers :  0.14 %
    Allowed  :  5.22 %
    Favored  : 94.64 %
  Rotamer:
    Outliers :  2.84 %
    Allowed  : 15.22 %
    Favored  : 81.94 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.00 (0.34), residues: 690
  helix:  None (None), residues: 0
  sheet:  0.75 (0.29), residues: 318
  loop : -0.66 (0.37), residues: 372

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP O  52 
 HIS   0.003   0.001   HIS H  93 
 PHE   0.013   0.001   PHE H  52A
 TYR   0.016   0.001   TYR M  32 
 ARG   0.003   0.000   ARG N  96 

*********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  1380 Ramachandran restraints generated.
    690 Oldfield, 0 Emsley, 690 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1380 Ramachandran restraints generated.
    690 Oldfield, 0 Emsley, 690 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  120 residues out of total 598 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 103
  time to evaluate  : 0.579 
Fit side-chains
   revert: symmetry clash
REVERT: H   18 LEU cc_start: 0.7957 (OUTLIER) cc_final: 0.7353 (tt)
REVERT: H   43 LYS cc_start: 0.7995 (mttp) cc_final: 0.7772 (mtmm)
REVERT: M   32 TYR cc_start: 0.7015 (m-10) cc_final: 0.6764 (m-10)
REVERT: M   85 GLU cc_start: 0.7792 (tm-30) cc_final: 0.7143 (tm-30)
REVERT: N    4 MET cc_start: 0.7103 (mmm) cc_final: 0.6621 (mmm)
REVERT: N   24 ARG cc_start: 0.7796 (mtp85) cc_final: 0.6487 (ttt90)
REVERT: N   89 GLN cc_start: 0.7500 (OUTLIER) cc_final: 0.6879 (tp40)
REVERT: N  102 THR cc_start: 0.7643 (OUTLIER) cc_final: 0.7399 (p)
REVERT: O   83 ARG cc_start: 0.8435 (mmm160) cc_final: 0.7785 (mmm160)
REVERT: P    4 MET cc_start: 0.8469 (OUTLIER) cc_final: 0.7714 (mtm)
  outliers start: 17
  outliers final: 11
  residues processed: 114
  average time/residue: 0.2248
  time to fit residues: 31.8429
Evaluate side-chains
  106 residues out of total 598 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 91
  time to evaluate  : 0.734 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain H residue   18 LEU
Chi-restraints excluded: chain H residue   31 THR
Chi-restraints excluded: chain H residue   93 HIS
Chi-restraints excluded: chain L residue   74 THR
Chi-restraints excluded: chain M residue   69 ILE
Chi-restraints excluded: chain N residue   74 THR
Chi-restraints excluded: chain N residue   89 GLN
Chi-restraints excluded: chain N residue  102 THR
Chi-restraints excluded: chain O residue   12 VAL
Chi-restraints excluded: chain O residue   48 VAL
Chi-restraints excluded: chain O residue   52 TRP
Chi-restraints excluded: chain O residue   78 VAL
Chi-restraints excluded: chain P residue    4 MET
Chi-restraints excluded: chain P residue    7 SER
Chi-restraints excluded: chain P residue   19 VAL
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 65
   random chunks:
   chunk 40 optimal weight:   20.0000
   chunk 15 optimal weight:    7.9990
   chunk 47 optimal weight:    6.9990
   chunk 22 optimal weight:    3.9990
   chunk 17 optimal weight:    0.9990
   chunk 35 optimal weight:    2.9990
   chunk 59 optimal weight:    1.9990
   chunk 61 optimal weight:   10.0000
   chunk 12 optimal weight:    2.9990
   chunk 64 optimal weight:    4.9990
   chunk 8 optimal weight:    6.9990
   overall best weight:    2.5990

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Flipped N/Q/H residues before XYZ refinement:
G 109 ASN
M   1 GLN
M 105 GLN
** O  76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4062 r_free = 0.4062 target = 0.159439 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3731 r_free = 0.3731 target = 0.131218 restraints weight = 7494.643|
|-----------------------------------------------------------------------------|
r_work (start): 0.3730 rms_B_bonded: 2.47
r_work: 0.3616 rms_B_bonded: 2.99 restraints_weight: 0.5000
r_work: 0.3465 rms_B_bonded: 4.96 restraints_weight: 0.2500
r_work (final): 0.3465
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7588
moved from start:          0.5326

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.087   5643  Z= 0.343
  Angle     :  0.645   7.014   7653  Z= 0.349
  Chirality :  0.047   0.156    812
  Planarity :  0.005   0.046    983
  Dihedral  :  5.186  50.182    774
  Min Nonbonded Distance : 2.486

Molprobity Statistics.
  All-atom Clashscore : 12.52
  Ramachandran Plot:
    Outliers :  0.14 %
    Allowed  :  7.97 %
    Favored  : 91.88 %
  Rotamer:
    Outliers :  4.01 %
    Allowed  : 15.22 %
    Favored  : 80.77 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.34 (0.34), residues: 690
  helix:  None (None), residues: 0
  sheet:  0.41 (0.29), residues: 324
  loop : -0.80 (0.36), residues: 366

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.019   0.002   TRP O  36 
 HIS   0.009   0.003   HIS H  93 
 PHE   0.018   0.003   PHE M  52A
 TYR   0.028   0.002   TYR N  49 
 ARG   0.005   0.001   ARG L  61 

*********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  1380 Ramachandran restraints generated.
    690 Oldfield, 0 Emsley, 690 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1380 Ramachandran restraints generated.
    690 Oldfield, 0 Emsley, 690 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  123 residues out of total 598 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 99
  time to evaluate  : 0.621 
Fit side-chains
   revert: symmetry clash
REVERT: H   18 LEU cc_start: 0.8074 (OUTLIER) cc_final: 0.7407 (tt)
REVERT: H   43 LYS cc_start: 0.8086 (mttp) cc_final: 0.7788 (mtmm)
REVERT: L   79 GLN cc_start: 0.8062 (mm-40) cc_final: 0.7711 (mm-40)
REVERT: M   32 TYR cc_start: 0.7497 (m-10) cc_final: 0.7260 (m-10)
REVERT: M   85 GLU cc_start: 0.7796 (tm-30) cc_final: 0.7024 (tm-30)
REVERT: N    4 MET cc_start: 0.7117 (mmm) cc_final: 0.6665 (mmm)
REVERT: N   89 GLN cc_start: 0.7636 (OUTLIER) cc_final: 0.6944 (tp40)
REVERT: N  102 THR cc_start: 0.7805 (OUTLIER) cc_final: 0.7445 (p)
REVERT: O  107 THR cc_start: 0.8060 (OUTLIER) cc_final: 0.7790 (t)
REVERT: P    3 GLN cc_start: 0.7262 (mp10) cc_final: 0.6674 (mp10)
REVERT: P   72 THR cc_start: 0.8297 (m) cc_final: 0.7765 (p)
  outliers start: 24
  outliers final: 16
  residues processed: 113
  average time/residue: 0.2213
  time to fit residues: 31.1321
Evaluate side-chains
  116 residues out of total 598 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 96
  time to evaluate  : 0.560 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain G residue  109 ASN
Chi-restraints excluded: chain H residue   18 LEU
Chi-restraints excluded: chain H residue   31 THR
Chi-restraints excluded: chain H residue   93 HIS
Chi-restraints excluded: chain L residue   26 SER
Chi-restraints excluded: chain L residue   58 VAL
Chi-restraints excluded: chain L residue   74 THR
Chi-restraints excluded: chain M residue   69 ILE
Chi-restraints excluded: chain N residue   74 THR
Chi-restraints excluded: chain N residue   89 GLN
Chi-restraints excluded: chain N residue  102 THR
Chi-restraints excluded: chain O residue    7 SER
Chi-restraints excluded: chain O residue   12 VAL
Chi-restraints excluded: chain O residue   48 VAL
Chi-restraints excluded: chain O residue   78 VAL
Chi-restraints excluded: chain O residue  107 THR
Chi-restraints excluded: chain P residue    4 MET
Chi-restraints excluded: chain P residue    7 SER
Chi-restraints excluded: chain P residue   19 VAL
Chi-restraints excluded: chain P residue   90 GLU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 65
   random chunks:
   chunk 59 optimal weight:    0.9980
   chunk 57 optimal weight:    4.9990
   chunk 30 optimal weight:    0.0470
   chunk 3 optimal weight:    0.0670
   chunk 32 optimal weight:    5.9990
   chunk 18 optimal weight:    3.9990
   chunk 46 optimal weight:    0.0770
   chunk 15 optimal weight:    4.9990
   chunk 47 optimal weight:    0.7980
   chunk 26 optimal weight:    0.9990
   chunk 58 optimal weight:    0.9990
   overall best weight:    0.3974

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Flipped N/Q/H residues before XYZ refinement:
G 109 ASN
M 105 GLN
** O  76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4143 r_free = 0.4143 target = 0.164404 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3816 r_free = 0.3816 target = 0.135598 restraints weight = 7896.337|
|-----------------------------------------------------------------------------|
r_work (start): 0.3819 rms_B_bonded: 2.57
r_work: 0.3686 rms_B_bonded: 3.28 restraints_weight: 0.5000
r_work (final): 0.3686
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7387
moved from start:          0.5610

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.035   5643  Z= 0.158
  Angle     :  0.583   7.545   7653  Z= 0.315
  Chirality :  0.045   0.140    812
  Planarity :  0.004   0.038    983
  Dihedral  :  4.979  47.296    774
  Min Nonbonded Distance : 2.507

Molprobity Statistics.
  All-atom Clashscore : 11.13
  Ramachandran Plot:
    Outliers :  0.14 %
    Allowed  :  5.65 %
    Favored  : 94.20 %
  Rotamer:
    Outliers :  2.51 %
    Allowed  : 16.89 %
    Favored  : 80.60 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.07 (0.34), residues: 690
  helix:  None (None), residues: 0
  sheet:  0.75 (0.29), residues: 318
  loop : -0.76 (0.36), residues: 372

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.020   0.002   TRP O  36 
 HIS   0.003   0.001   HIS H  93 
 PHE   0.020   0.002   PHE M  29 
 TYR   0.015   0.001   TYR M  32 
 ARG   0.007   0.001   ARG N  96 

********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  1380 Ramachandran restraints generated.
    690 Oldfield, 0 Emsley, 690 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1380 Ramachandran restraints generated.
    690 Oldfield, 0 Emsley, 690 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  109 residues out of total 598 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 94
  time to evaluate  : 0.623 
Fit side-chains
   revert: symmetry clash
REVERT: H   18 LEU cc_start: 0.8173 (OUTLIER) cc_final: 0.7581 (tt)
REVERT: H   43 LYS cc_start: 0.8098 (mttp) cc_final: 0.7887 (mtmm)
REVERT: L    4 MET cc_start: 0.8184 (mmm) cc_final: 0.7845 (mmm)
REVERT: M   32 TYR cc_start: 0.6696 (m-10) cc_final: 0.6348 (m-10)
REVERT: N    4 MET cc_start: 0.7026 (mmm) cc_final: 0.6542 (mmm)
REVERT: N   24 ARG cc_start: 0.7714 (mtp85) cc_final: 0.6572 (ttt90)
REVERT: N   89 GLN cc_start: 0.7365 (OUTLIER) cc_final: 0.6998 (tp40)
REVERT: N  102 THR cc_start: 0.7632 (OUTLIER) cc_final: 0.7351 (p)
REVERT: P    4 MET cc_start: 0.8213 (OUTLIER) cc_final: 0.7420 (mtm)
REVERT: P   72 THR cc_start: 0.8120 (m) cc_final: 0.7628 (p)
  outliers start: 15
  outliers final: 9
  residues processed: 106
  average time/residue: 0.2284
  time to fit residues: 29.7671
Evaluate side-chains
  98 residues out of total 598 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 85
  time to evaluate  : 0.576 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain H residue   18 LEU
Chi-restraints excluded: chain H residue   31 THR
Chi-restraints excluded: chain H residue   93 HIS
Chi-restraints excluded: chain M residue   69 ILE
Chi-restraints excluded: chain N residue   74 THR
Chi-restraints excluded: chain N residue   89 GLN
Chi-restraints excluded: chain N residue  102 THR
Chi-restraints excluded: chain O residue   12 VAL
Chi-restraints excluded: chain O residue   48 VAL
Chi-restraints excluded: chain O residue   78 VAL
Chi-restraints excluded: chain P residue    4 MET
Chi-restraints excluded: chain P residue    7 SER
Chi-restraints excluded: chain P residue   19 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 65
   random chunks:
   chunk 38 optimal weight:    0.4980
   chunk 62 optimal weight:   10.0000
   chunk 44 optimal weight:    0.9990
   chunk 16 optimal weight:   20.0000
   chunk 61 optimal weight:    0.9990
   chunk 35 optimal weight:    0.5980
   chunk 5 optimal weight:    0.9980
   chunk 52 optimal weight:    7.9990
   chunk 57 optimal weight:    6.9990
   chunk 7 optimal weight:    6.9990
   chunk 25 optimal weight:    0.8980
   overall best weight:    0.7982

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Flipped N/Q/H residues before XYZ refinement:
G 109 ASN
M 105 GLN
** O  76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4115 r_free = 0.4115 target = 0.161802 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3800 r_free = 0.3800 target = 0.133904 restraints weight = 7824.319|
|-----------------------------------------------------------------------------|
r_work (start): 0.3809 rms_B_bonded: 2.47
r_work: 0.3673 rms_B_bonded: 3.25 restraints_weight: 0.5000
r_work (final): 0.3673
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7402
moved from start:          0.5744

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041   5643  Z= 0.183
  Angle     :  0.583   7.157   7653  Z= 0.315
  Chirality :  0.046   0.140    812
  Planarity :  0.004   0.037    983
  Dihedral  :  4.841  45.468    774
  Min Nonbonded Distance : 2.498

Molprobity Statistics.
  All-atom Clashscore : 10.85
  Ramachandran Plot:
    Outliers :  0.14 %
    Allowed  :  7.10 %
    Favored  : 92.75 %
  Rotamer:
    Outliers :  2.34 %
    Allowed  : 17.56 %
    Favored  : 80.10 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.04 (0.35), residues: 690
  helix:  None (None), residues: 0
  sheet:  0.81 (0.29), residues: 318
  loop : -0.68 (0.37), residues: 372

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.001   TRP O  36 
 HIS   0.005   0.001   HIS H  93 
 PHE   0.030   0.002   PHE M  52A
 TYR   0.015   0.001   TYR P  91 
 ARG   0.004   0.000   ARG O  83 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2873.60 seconds
wall clock time: 51 minutes 40.54 seconds (3100.54 seconds total)